Genome-Wide Identification and Characterization of AGO, DCL, and RDR Gene Families in Siraitia grosvenorii
Abstract
1. Introduction
2. Results
2.1. Identification and Structural Analysis of SgAGO, SgDCL, and SgRDR Genes in S. grosvenorii
2.2. Motif and Domain Analyses of SgAGO, SgDCL, and SgRDR in S. grosvenorii
2.3. Phylogenetic Analysis of SgAGO, SgDCL, and SgRDR in S. grosvenorii and Other Plant Species
2.4. Protein–Protein Interactions of SgAGO, SgDCL, and SgRDR
2.5. Cis-Acting Element Analysis in SgAGO, SgDCL, and SgRDR Genes
2.6. Tissue-Specific Expression Patterns of SgAGO, SgDCL, and SgRDR Genes
3. Discussion
3.1. Evolution and Functional Divergence Mechanisms of RNAi Pathway Gene Families
3.2. Cis-Acting Element Analysis Reveals Hormonal and Stress Response Regulatory Mechanisms of RNAi Core Genes in S.grosvenorii
3.3. Functional Divergence of AGO, DCL, and RDR Gene Families in Tissue-Specific Expression and Developmental Regulation in S. grosvenorii
4. Materials and Methods
4.1. Plant Material
4.2. Data Collection and Identification of AGO, DCL, and RDR in S. grosvenorii
4.3. Phylogenetic Tree Construction
4.4. Conserved Motif and Gene Structure Analysis
4.5. Gene Expression Analysis
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
Abbreviations
ABA | Abscisic Acid |
AGO | Argonaute |
DAP | Days After Pollination |
DCL | Dicer-like |
DSRM | Double-stranded RNA-binding domain |
dsRNA | Double-stranded RNA |
GA | Gibberellin |
GRAVY | grand average of hydropathicity |
ICL | Isocitrate lyase |
MeJA | Methyl Jasmonate |
MEME | Multiple Em for Motif Elicitation |
ORF | open reading frame |
PPI | Protein–protein interaction |
qRT-PCR | Quantitative real-time PCR |
RDR | RNA-dependent RNA polymerase |
RdDM | RNA-directed DNA methylation |
RNAi | RNA interference |
RISC | RNA-induced silencing complex |
SA | Salicylic Acid |
sRNAs | small RNAs |
siRNAs | small interfering RNAs |
UBQ | Ubiquitin |
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Gene Name | Gene Locus | Number of Amino Acids | Molecular Weight (kDa) | Theoretical pI | Grand Average of Hydropathicity (GRAVY) | Predicted Subcellular Localization |
---|---|---|---|---|---|---|
SgAGO1 | Chr09.g17302 | 1056 | 117.11 | 9.31 | −0.50 | Nucleus |
SgAGO4 | Chr06.g10665 | 1014 | 113.60 | 8.79 | −0.32 | Cell membrane, chloroplast, and nucleus |
SgAGO5 | Chr09.g16238 | 967 | 107.54 | 9.48 | −0.41 | Nucleus |
SgAGO7 | Chr10.g18565 | 1018 | 115.58 | 9.37 | −0.40 | Chloroplast and nucleus |
SgAGO10.1 | Chr08.g15010 | 927 | 105.33 | 9.22 | −0.39 | Cell membrane and nucleus |
SgAGO10.2 | Chr03.g06089 | 984 | 110.63 | 9.33 | −0.44 | Nucleus |
SgDCL1 | Chr03.g06642 | 1952 | 219.66 | 5.87 | −0.44 | Nucleus |
SgDCL2 | Chr08.g14552 | 1628 | 183.60 | 8.55 | −0.060 | Nucleus |
SgDCL3 | Chr02.g03104 | 1708 | 191.74 | 6.39 | −0.16 | Nucleus |
SgDCL4 | Chr08.g15125 | 1651 | 186.62 | 6.30 | −0.27 | Nucleus |
SgRDR1.1 | Chr10.g17889 | 1112 | 127.79 | 7.89 | −0.32 | Chloroplast |
SgRDR1.2 | Chr01.g01240 | 1123 | 128.68 | 8.11 | −0.38 | Chloroplast and nucleus |
SgRDR1.3 | Chr10.g17890 | 1133 | 129.16 | 8.30 | −0.29 | Chloroplast |
SgRDR2 | Chr08.g15576 | 1121 | 128.81 | 6.72 | −0.29 | Nucleus |
SgRDR5 | Chr08.g14932 | 1026 | 116.35 | 7.89 | −0.30 | Chloroplast |
SgRDR6 | Chr02.g03034 | 1194 | 135.98 | 6.97 | −0.30 | Chloroplast and nucleus |
Query Index | Query Item | Preferred Name | Identity (%) | Bitscore |
---|---|---|---|---|
1 | SgAGO1 | AtAGO1 | 82.8 | 1565.8 |
2 | SgAGO4 | AtAGO4 | 72.9 | 1357.8 |
3 | SgAGO5 | AtAGO5 | 67 | 1164.1 |
4 | SgAGO7 | AtAGO7 | 70.2 | 1269.6 |
5 | SgAGO10.1 | AtAGO10 | 74.5 | 1348.6 |
6 | SgAGO10.2 | AtAGO10 | 82.6 | 1661.4 |
7 | SgDCL1 | AtDCL1 | 71.7 | 2708.3 |
8 | SgDCL2 | AtDCL2 | 57.8 | 1550 |
9 | SgDCL3 | AtDCL3 | 47.8 | 1435.6 |
10 | SgDCL4 | AtDCL4 | 55.4 | 1721.8 |
11 | SgRDR1.1 | AtRDR1 | 61.2 | 1370.5 |
12 | SgRDR1.2 | AtRDR1 | 58.6 | 1266.9 |
13 | SgRDR1.3 | AtRDR1 | 63.7 | 1444.9 |
14 | SgRDR2 | AtRDR2 | 61.2 | 1403.7 |
15 | SgRDR5 | AtRDR5 | 51.3 | 866.3 |
16 | SgRDR6 | AtRDR6 | 67 | 1674.1 |
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Zang, Y.; Wang, C.; Su, J.; Mo, C.; Xie, L.; Luo, Z.; Ma, X. Genome-Wide Identification and Characterization of AGO, DCL, and RDR Gene Families in Siraitia grosvenorii. Int. J. Mol. Sci. 2025, 26, 5301. https://doi.org/10.3390/ijms26115301
Zang Y, Wang C, Su J, Mo C, Xie L, Luo Z, Ma X. Genome-Wide Identification and Characterization of AGO, DCL, and RDR Gene Families in Siraitia grosvenorii. International Journal of Molecular Sciences. 2025; 26(11):5301. https://doi.org/10.3390/ijms26115301
Chicago/Turabian StyleZang, Yimei, Chongnan Wang, Jiaxian Su, Changming Mo, Lei Xie, Zuliang Luo, and Xiaojun Ma. 2025. "Genome-Wide Identification and Characterization of AGO, DCL, and RDR Gene Families in Siraitia grosvenorii" International Journal of Molecular Sciences 26, no. 11: 5301. https://doi.org/10.3390/ijms26115301
APA StyleZang, Y., Wang, C., Su, J., Mo, C., Xie, L., Luo, Z., & Ma, X. (2025). Genome-Wide Identification and Characterization of AGO, DCL, and RDR Gene Families in Siraitia grosvenorii. International Journal of Molecular Sciences, 26(11), 5301. https://doi.org/10.3390/ijms26115301